Course Intro
Practical Computing Skills for Omics Data (PLNTPTH 5004)
2025-08-26
The Unix shell & shell scripts
The Unix shell (or the “Terminal”) is a command-line interface to computers.
Being able to use the Unix shell is a fundamental skill when working with omics data, for example because many of the specialized analysis software must be run using the shell.
- You’ll spend a lot of time with the Unix shell, starting next week.
- You’ll also write shell scripts, and will use an editor called VS Code for this and other purposes.
Bash (shell language)
VS Code
Project organization & documentation
Good project organization & documentation is a necessary starting point for reproducible research.
You’ll learn best practices for project organization, file naming, etc.
You’ll learn how to manage your data and software
To document and report what you are doing, you’ll use Markdown files.
Markdown
Version control with Git and GitHub
Using version control, you can more effectively keep track of project progress, collaborate, share code, revisit earlier versions, and undo.
Git is the version control software we will use,
and GitHub is the website that hosts Git projects (repositories).You’ll also use Git + GitHub to hand in your graded assignments.
High-performance computing with OSC
Thanks to supercomputer resources, you can work with very large datasets at speed — running up to 100s of analyses in parallel, and using much larger amounts of memory and storage space than a personal computer has.
- We will use OSC throughout the course, and you’ll get a brief intro to it this week
- In week 5, you’ll learn how to manage data and software at OSC (e.g. with Conda)
- In week 6, you’ll learn to submit shell scripts as OSC “batch jobs” with Slurm
Automated workflow management
Omics data analyses typically consist of many consecutive steps.
Using a workflow written with a workflow manager, you can run and rerun an entire analysis pipeline with a single command (and much more).
- You’ll use the workflow language Nextflow to build your pipelines
- You will also learn how to use comprehensive, best-practice omics data Nextflow pipelines produced by the nf-core initiative
The R language
While the Unix shell, and software that is run through the Unix shell, is best used for the initial (algorithmic) processing steps of omics data, R is probably the most prominent language in the more “downstream” and often statistical analysis and visualization of omics data.
In this course, you will learn the basics of R, how to visualize data in R, and how you can use specialized packages for omics data analyis.
R vs. Python
Python is also commonly used but I believe that altogether, R is a far better choice for this course. On the other, Python is a great follow-up language to learn for those seeking to specialize in bioinformatics.